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- PDB-9ei6: PasI from Photorhabdus asymbiotica bound to Fe(II) and alpha-keto... -

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Basic information

Entry
Database: PDB / ID: 9ei6
TitlePasI from Photorhabdus asymbiotica bound to Fe(II) and alpha-ketoglutarate
ComponentsProlyl 4-hydroxylase alpha subunit domain-containing protein
KeywordsOXIDOREDUCTASE / iron / polyoxin / biosynthesis / nucleotide / high-carbon sugar
Function / homology
Function and homology information


L-ascorbic acid binding / dioxygenase activity / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen / iron ion binding
Similarity search - Function
Prolyl 4-hydroxylase alpha subunit, Fe(2+) 2OG dioxygenase domain / 2OG-Fe(II) oxygenase superfamily / Prolyl 4-hydroxylase, alpha subunit / Prolyl 4-hydroxylase alpha subunit homologues.
Similarity search - Domain/homology
2-OXOGLUTARIC ACID / : / DI(HYDROXYETHYL)ETHER / Prolyl 4-hydroxylase alpha subunit domain-containing protein
Similarity search - Component
Biological speciesPhotorhabdus asymbiotica (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.44 Å
AuthorsDong, J. / Boal, A.K.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)5R35GM119707-09 United States
CitationJournal: J.Am.Chem.Soc. / Year: 2025
Title: Unusual O-H Activation-Initiated C-C Bond Cleavage Reaction by a Nonheme Fe Enzyme in Antifungal Nucleoside Biosynthesis.
Authors: Du, Y. / Dong, J. / Draelos, M.M. / Collazo-Perez, L.N. / Majer, S.H. / Boal, A.K. / Yokoyama, K.
History
DepositionNov 25, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 20, 2025Provider: repository / Type: Initial release
Revision 1.1Aug 27, 2025Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Prolyl 4-hydroxylase alpha subunit domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,60013
Polymers26,4431
Non-polymers1,15712
Water4,324240
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)55.587, 105.336, 39.997
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-611-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Prolyl 4-hydroxylase alpha subunit domain-containing protein


Mass: 26442.916 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Photorhabdus asymbiotica (bacteria) / Gene: sanC, PAU_00621 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: C7BKM7

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Non-polymers , 6 types, 252 molecules

#2: Chemical ChemComp-AKG / 2-OXOGLUTARIC ACID


Mass: 146.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H6O5 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C4H10O3
#6: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 240 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.21 Å3/Da / Density % sol: 44.45 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: PasI was co-crystallized with Fe(II) and alpha-ketoglutarate in a hanging drop vapor diffusion experiment. The protein solution [10 mg/mL of His-PasI, 1 equiv of ferrous ammonium sulfate, 5 ...Details: PasI was co-crystallized with Fe(II) and alpha-ketoglutarate in a hanging drop vapor diffusion experiment. The protein solution [10 mg/mL of His-PasI, 1 equiv of ferrous ammonium sulfate, 5 equiv of sodium alpha-ketoglutarate, 17 mM Tris pH 7.6, and 2% (v/v) glycerol] was mixed with a reservoir solution [0.1 M Bis-Tris (pH 5.5), 0.1 M Li2SO4, and 19.5% (w/v) PEG 3350] in a 2:1 ratio.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Aug 6, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.44→31.03 Å / Num. obs: 40679 / % possible obs: 93.8 % / Redundancy: 6.6 % / CC1/2: 0.998 / Net I/σ(I): 11.5
Reflection shellResolution: 1.44→1.49 Å / Num. unique obs: 2629 / CC1/2: 0.318

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XDSdata scaling
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.44→31.85 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2059 1954 4.8 %
Rwork0.1732 --
obs0.1748 40678 93.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.44→31.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1749 0 67 240 2056
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0111873
X-RAY DIFFRACTIONf_angle_d1.1012526
X-RAY DIFFRACTIONf_dihedral_angle_d14.761692
X-RAY DIFFRACTIONf_chiral_restr0.109254
X-RAY DIFFRACTIONf_plane_restr0.011323
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.44-1.480.3485900.31271663X-RAY DIFFRACTION57
1.48-1.520.29281050.27342185X-RAY DIFFRACTION75
1.52-1.560.28771270.24392497X-RAY DIFFRACTION86
1.56-1.610.24491380.22272780X-RAY DIFFRACTION95
1.61-1.670.24351450.19982879X-RAY DIFFRACTION99
1.67-1.740.221480.17832910X-RAY DIFFRACTION100
1.74-1.810.20031470.17232927X-RAY DIFFRACTION100
1.81-1.910.18711470.16932921X-RAY DIFFRACTION100
1.91-2.030.19011480.1612919X-RAY DIFFRACTION100
2.03-2.190.19351470.16212930X-RAY DIFFRACTION100
2.19-2.410.18471510.15782961X-RAY DIFFRACTION100
2.41-2.750.1911500.17872983X-RAY DIFFRACTION100
2.75-3.470.2071510.16883016X-RAY DIFFRACTION100
3.47-31.850.20471600.16073153X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.6362-0.4886-0.05522.404-0.70341.16650.09780.16490.0375-0.0509-0.089-0.0944-0.09170.045-0.01360.1323-0.0121-0.01990.1125-0.03410.12516.834816.12210.4241
20.8006-0.0645-0.04650.98990.05281.18120.00570.0263-0.0069-0.0204-0.0394-0.04250.04420.06520.03470.0877-0.003-0.00360.10940.00740.13069.46615.328414.7196
32.2966-1.4323-0.10851.2752-0.05210.21740.11160.0922-0.0527-0.16-0.04880.1010.034-0.0361-0.09980.1404-0.0178-0.00620.1405-0.00880.1624-11.370619.0416.0726
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 35 through 74 )
2X-RAY DIFFRACTION2chain 'A' and (resid 75 through 226 )
3X-RAY DIFFRACTION3chain 'A' and (resid 11 through 34 )

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